2015-11-12 5:51 GMT-07:00 Rom <[email protected]>: > Hello all! > > I have a small query, and I couldn't find it anywhere else on this page. > > I'm doing hybrid FM of hexane (256 molecules in a box), where boltzmann > inversion for the bonded, and FM for the non-bonded. > My simulation appeared to show all of my hexane molecules clumping together > (literally a giant ball of dense hexanes). > > I compared my non bonded potential e.g. A-A, to the potential given in the > paper: > > Victor Ruehle, Christoph Junghans, Macrolmol. Theory Simul. 2011, 20, > 472-477 (Hybrid approaches to coarse-graining using the VOTCA package: > Liquid Hexane) > > I have an attractive well depth of -20kj/mol (attached, plot column 1 and > 6), whereas the potential in the paper has a well depth of -1 kj/mol, so > mine is far too attractive (which explains the extreme aggregation)! Even my > slight repulsive bump at the zero line is almost 0.8 kj/mol. > > Is there any obvious reason why my potential could be this off? Is it an > effect of maybe how I choose my grid size, or blocking averages when force > matching? Did you follow the hexane/hybrid_force_matching tutorial? <https://github.com/votca/csg-tutorials/tree/master/hexane/hybrid_force_matching>
Grid size, or blocking averages when force matching only matter if you running low on statistics. I seems to me, you might have forgot to the rerun step using mdrun to subtract the force. Christoph > > If you need anymore files or details, please just let me know, I will be > happy to provide them! and thank you for all the help :D > > Many thanks > Rom > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
